rs10088180

Variant names:

• chr8-18370607-A-G
• rs10088180
• ENST00000523491.1:n.1A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000523491.1(NATP):​n.1A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.649 in 153,810 control chromosomes in the GnomAD database, including 33,032 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.65 (33002 hom., cov: 32)
  • Exomes 𝑓: 0.15 (30 hom.)
• Consequence: NATP ENST00000523491.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.53
• Publications: 5 publications found

Genes affected

NATP (HGNC:15): (N-acetyltransferase pseudogene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NATP		n.18370607A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NATP	ENST00000523491.1	n.1A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99457 AN: 151962 Hom.: 32992 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.651

GnomAD4 exome AF: 0.147 AC: 254 AN: 1730 Hom.: 30 Cov.: 0 AF XY: 0.178 AC XY: 174 AN XY: 980

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.125 AC: 5 AN: 40

American (AMR) AF: 0.0603 AC: 21 AN: 348

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12

East Asian (EAS) AF: 0.0116 AC: 3 AN: 258

South Asian (SAS) AF: 0.0932 AC: 11 AN: 118

European-Finnish (FIN) AF: 0.199 AC: 37 AN: 186

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.219 AC: 153 AN: 698

Other (OTH) AF: 0.343 AC: 24 AN: 70

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.654 AC: 99508 AN: 152080 Hom.: 33002 Cov.: 32 AF XY: 0.646 AC XY: 48006 AN XY: 74344

African (AFR) AF: 0.650 AC: 26931 AN: 41450

American (AMR) AF: 0.533 AC: 8141 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2375 AN: 3470

East Asian (EAS) AF: 0.349 AC: 1806 AN: 5174

South Asian (SAS) AF: 0.661 AC: 3189 AN: 4826

European-Finnish (FIN) AF: 0.656 AC: 6927 AN: 10566

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47833 AN: 68004

Other (OTH) AF: 0.646 AC: 1365 AN: 2112

Alfa AF: 0.682 Hom.: 28629

Bravo AF: 0.641

Asia WGS AF: 0.502 AC: 1746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	13
DANN	Benign	0.59
PhyloP100		6.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10088180; hg19: chr8-18228116;